School of Medicine

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Current Role at Stanford
I joined Stanford in Oct 2012 as the Director of Bioinformatics at Stanford Center for Genomics and Personalized Medicine (SCGPM). My role at the Center is to develop and lead the bioinformatics team and establish a world class omics and other types of biomedical data analysis facility.

Our bioinformatics team is comprised of a dozen scientists and software engineers. Together the team has a wide range of skill sets including various omics, computational biology, machine learning, software engineering, data management, Databases, Visualization, High Performance Computing, IT, and Cloud DevOps. The team is currently supporting several large scale research and clinical programs at Stanford including prestigious consortium efforts and inter-disciplinary collaborations.

Among our various efforts is Genetics Bioinformatics Service Center, a Big Data Biomedical and Bioinformatics Core Facility, created in 2013 to streamline the availability of infrastructure to the wider biomedical community at Stanford and our research affiliates. The Core facility provides best-in-class high performance computational systems, scalable Cloud computing and cutting edge bioinformatics services for the Stanford community. The core operates under Department of Genetics and is overseen by Office of Dean. The services are NIH dbGaP and SoM security requirements compliant. We also provide a comprehensive analytical stack with over 400 applications installed centrally on the cluster for ease of use by researchers. Currently the Core supports over 75 labs and 750 researchers.

Current Research and Scholarly Interests
We are using Saccharomyces cerevisiae and Human to conduct whole genome analysis projects. The yeast genome sequence has approximately 6,000 genes. We have made a set of haploid and diploid strains (21,000) containing a complete deletion of each gene. In order to facilitate whole genome analysis each deletion is molecularly tagged with a unique 20-mer DNA sequence. This sequence acts as a molecular bar code and makes it easy to identify the presence of each deletion.

Bio
I'm a Senior Research Scientist in the Department of Genetics at Stanford University, currently working in the laboratories of Dr. Mike Snyder and Dr. Gavin Sherlock. I received my A.B. in Botany at UC Berkeley, and my Ph.D. in Biological Chemistry at Harvard University, where I studied yeast telomeres in the laboratory of Dr. Jack Szostak. My recent research has focused on using whole-genome DNA and RNA sequencing, ChIP-Seq, array-CGH, and other “omics” methods to broadly explore evolution in yeast, and particularly the genome structures and genome evolution of industrial yeasts (lager, ale, wine, ethanol, bread).